forked from richfitz/diversitree
/
ChangeLog
1341 lines (851 loc) · 42.1 KB
/
ChangeLog
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
2013-06-13 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* For current changes, see github page.
2012-03-26 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/model-mkn-multitrait.R, R/model-musse-multitrait.R: restore
'pars.only' argument to multitrait function, as this is useful for
priors.
2012-03-25 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/check.R: Negative branch length check was being skipped.
* R/diversitree-branches.R: More safety checking for ultrametric
trees, in preparation of allowing eventual non-ultrametric trees
for more models.
* R/model-bm-direct.R: Clarify branches calculations.
* R/plot-alt-extra.R: add drop=TRUE to prevent de-dataframing.
* R/profiles-plot.R: More automation (legends, argument names, and
opacity).
2012-03-23 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/check.R: typo in check.scalar(), more informative error in
check.loaded.symbol().
* R/cvodes.R: function 'cvodes.headers()' to generate appropriate
headers for using cvodes-based integrators.
* R/deSolve.R: Function arguments were transposed! Plus pure-R
ode generation.
* R/diversitree-branches.R: Support for pure-R odes (replacing
make.branches.lsoda and all.branches.lsoda). Simplify argument
list for dt.tips.grouped().
* R/model-bd-ode.R, R/model-mkn-ode.R, R/model-musse-multitrait.R:
use new dt.tips.grouped().
2012-03-22 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* Too many files to list: huge rewrite of most behind the scenes
stuff. New VCV based OU calculations.
2012-03-15 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/asr-musse.R: Updates so that time-varying musse models are
possible.
* R/check.R: Fix handling of clade.trees in bd models.
* R/model-bd-ode.R: Reorder error checking
* R/model-bd.R: Give up on special yule model ML treatment
* R/model-musse-t.R: Improve logic around parameter checking --
avoid checking constant parameters twice, check time varying
ones.
* R/sim-character.R: Unfortunately, this was broken on release.
Fixed now.
* Updates so that diversitree compiles and passes check on CRAN.
2012-03-13 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/model-bd*.R: Combined ode and Nee BD calculations.
* DESCRIPTION: Bump to 0.9-1, add mention of Classe and BiSSE-ness
* NAMESPACE: More imports
* R/check.R: check.control.continuous, for checking vcv/direct
switch for BM methods.
* R/diversitree-branches.R: whitespace?
* R/model-bisseness-unresolved.R: Added unresolved clade support
for BiSSE-ness (from Sally Otto)
* R/model-bisseness.R: Changes to allow unresolved clades, and
other minor tweaks.
* R/model-bm.R: switch to 'control' based method switching.
* R/model-classe.R: Added
* R/model-geosse-split.R: Updated to work with new split
functions.
* R/model-geosse.R: A ton of little updates to work better with
new support functions.
* R/model-ou.R: Added control argument, though it does nothing.
* R/plot-alt-extra.R: New trait.plot() function.
* R/plot-alt-util.R: New unexported "filled.arcs" function.
* R/plot-alt.: Minor tweaks.
* R/simulate-musse.R: Simulation support for musse.multitrait
trees.
* R/util.R: uniform prior was incorrect (but not in a way that
would affect calculations).
* man/make.bisseness.Rd: New documentation.
* man/make.bm.Rd: Updated to reflect control change.
* man/make.classe.Rd: New documentation
* man/make.geosse.Rd: Substantial updates
* man/simulate.Rd: Updates for tree.musse.multitrait
* man/trait.plot.Rd: New documentation
* src/bucexp.c: Remove print statements
* src/classe-eqs.c: New
* src/cvodes/*: Remapped printf -> Rprintf
* src/geosse-eqs.c: Small tidy up
* src/nuexp.f: BiSSE-ness unresolved clade calculations.
2012-02-23 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: Bump to 0.8-4
* NAMESPACE: Updated to add bisseness
* R/mcmc.R: Additional argument checking.
* R/mle.R: Hardened version of anova.fit.mle that attempts to
check that models are truely nested.
* R/model-bd.R: find.mle.yule now returns class "fit.mle.bd" so
that it is clear that it can be compared against a bd fit.
* R/model-bisseness.R: Added skeleton for "unresolved" branches
function to clear up code.
* R/simulation.R: Added "bisseness" to list of possible tree types
that can be simulated.
* man/find.mle.Rd: Documented additional restrictions on model
comparison.
* man/make.bisse.Rd: Updated returned function definition.
* man/mcmc.Rd: Documented save.every/save.file arguments.
* man/simulate.Rd: Documented addition of bisseness simulator.
2012-02-22 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/model-bisseness.R: Added the "BiSSE-ness" model from Karen and Sally.
2012-02-13 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: Bump R dependency up, and add support for current
deSolve.
* R/combine.R: First import of experimental likelihood combining
functions.
* R/diversitree-branches.R: Simplify treatment of root node.
* R/mcmc.R: Simplify mcmc function exit, and add support for
saving progress to a csv file during a run.
* R/model-bm-vcv.R: Fix treatment of NULL/0 meserr.
* R/plot-alt-extra.R: Fix treatment of stored angles.
* R/plot-alt.R: Cosmetics
2012-01-05 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: Bump to 0.8-3
* NAMESPACE: New exports for mkn.ode, mkn.multitrait, ou,
geosse.split, sim.character, and others.
* R/asr-mkn.R: Adjust to the changes to mkn backends.
* R/check.R: BM parameter checking, split control checking.
* R/constrain.R: Constrained functions now handle additional
arguments.
* R/diversitree-branches-C.R: Fixed bug in cache translation for
some models (was failing to run previously).
* R/model-bisse-split.R: Abstract checking.
* R/model-bm-direct.R: New direct BM likelihood calculation (from
bbm).
* R/model-bm-vcv.R: Previous BM calculation
* R/model-bm.R: Now make.bm() has method argument to switch
between direct and vcv.
* R/model-geosse-split.R: Started adding (still unchecked).
* R/model-mkn-exp.R: Prevous mkn version (matrix exponentiation)
* R/model-mkn-multitrait.R: Multitrait version of the Mk model,
done as for MuSSE.
* R/model-mkn-ode.R: New ODE-based Mkn integrator, useful for high
k.
* R/model-mkn.R: Allows switching between ode and exp version.
* R/model-mkn-ode.R: ODE based branch-by-branch version of the Mk
model. This is needed for very large trait space where it is
much more efficient to compute exp(Qt).v without storing
Pij=exp(Qt) directly.
* R/model-mkn.R: Allow switching backends.
* R/model-musse-multitrait.R: Change mcmc defaults
* R/model-musse-split.R: Abstract checking
* R/model-ou.R: Branch-by-branch calculation of OU, from bbm.
* R/model-quasse-common.R: Bring up to date with BM changes.
* R/model-quasse-{fftC,fftR,mol}.R: Bunchn of changes to handling
of badly behaved branches -- now split branches into parts if
integration fails.
* R/model-quasse-split.R: Now does caching branches so that only
some parts of the variables may need recomputing. Will be
particularly useful during MCMC and ML searches with large
models.
* R/plot-alt.R: Fix x/y coordinates for fan plots.
* R/sim-character.R: Character simulation code.
* R/simulate-musse.R: Fixed bug that caused error when empty tree
was generated.
* R/split.R: Changes to allow caching branches.
* R/util.R: Uniform prior, and default setting function (modifies
a function's formals).
* man/*: Documentation updates.
* src/cvodes.c: Fixed compilation-preventing bug (reported by Jos
Kafer).
* src/mkn-eqs.c: Required support for the ODE based Mkn model.
2011-11-03 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/constrain.R: Allow variables used as constraints (on the RHS)
to be themselves constrained (on the LHS).
2011-10-13 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: bump to 0.8-1
* NAMESPACE: New asr methods declared
* R/asr-bisse-split.R, asr-musse-split.R: New asr methods
* R/asr-bisse.R: Minor clarification in code
* R/asr.R, R/model-bd-ode.R, R/model-bisse.R, R/model-geosse.R,
R/model-musse.R, R/t.R, R/td.R:
branches() now takes 'index' argument. Added.
* R/check.R: sampling.f check was incorrect.
* R/diversitree-branches.R: Added index argument to branches, and
other cleanup.
* R/model-bd-split.R: Cleanup
* R/model-bd-t.R: unresolved and sampling.f arguments were
transposed when checking, disabling sampling.f != 1. (reported by
Dan Rabosky).
* R/model-bisse-split.R, R/model-musse-split.R,
R/model-quasse-split.R: Reworked; should be more reliable now.
* R/model-quasse-common.R: Now allows different diffusion
parameters.
* R/model-quasse-fftC.R: Simpify away an old optimisation.
* R/model-quasse.R: Minor tidyup.
* R/plot-alt-extra.R, R/plot-alt-util.R: Pass additional arguments
of group.label.tip.rad() to radial.text() to text()
* R/split.R: Totally reworked.
* R/util.R: Updated to work with deSolve 1.10-3
* configure.ac: Revert to controllable strict gcc checking (off
again by default).
* man/*: Assorted documentation updates.
2011-07-11 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: bump to 0.7-6
* NAMESPACE: New "musse.multitrait" exports (see below)
* R/check.R: There was an error in checking states when
strict=FALSE (values were never checked to see if they were valid,
as was advertised). check.unresolved.bd added (taken from
make.bd, and used by make.bd.split).
* R/diversitree-branches.R: Individual tip conditions added for
make.branches.matrix. dt.tips.ordered() rewritten.
* R/history.R: Minor tweaks
* R/model-bd-split.R: Use with unresolved clades was totally
broken (but failed to even run, so no harm done).
* R/model-bd.R: Minor tweaks while tidying up model-bd-split.R
* R/model-musse-multitrait.R: Alternative reparametrisation of
MuSSE when the multistate character is really combinations of
binary traits.
* R/simulation.R: Simulation code was returning events in
incorrect order.
* man/*: minor documentation changes
* src/cvodes_asr_marginal.c,mkn.c,mkn.h: Tweaks to compile under
windows.
2011-06-03 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: bump to 0.7-4
* R/asr-bisse.R: General cleanup and remove obsolete options.
* R/asr-mkn.R: Cleanup, especially parameter handling and actual
simulation.
* R/asr-musse.R: General cleanup and remove obsolete options.
Simpler parameter handling.
* R/asr.R: Reimplimented asr on constrained models. General tidy
up.
* R/check.R: New BiSSE/MuSSE parameter checking that will end up
applied to more functions over time.
* R/constrain.R: Tidy up
* R/diversitree-branches-C.R: Moved do.marginal.asr.C into asr.R.
* R/diversitree-branches.R: Substantial simplification to
all.branches.matrix(). Removed cleanup().
* R/model-bisse-split.R: Tidy to parallel model-musse-split.R
* R/model-mkn.R: Cleanup, especially parameter handling.
* Other files: General cleanup
2011-06-01 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* Many files: reworked internals to use matrices rather than lists
where possible to simplify the ASR code. Slight efficiency gain,
too.
2011-05-31 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/asr-mkn.R: Faster joint and stochastic reconstructions through
the new C code; (still optional)
* R/asr.R: Faster joint reconstructions through the new C
code; (still optional)
* R/diversitree-branches.R: Prepping for big change
* R/mcmc.R: Additional ... arguments being passed to prior with
poor effects.
* R/model-mkn.R: No longer ever return lists as intermediate
output.
* R/util.R: Temporary fix for older R versions
2011-05-12 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: Bump to 0.7-2
* NAMESPACE: Actually export the make.asr.marginal functions
* R/asr-bisse.R, R/asr-musse.R: Tidy up, and enable CVODES to be
used for the ASR.
* R/check.R;R/cvodes.R: check to see if we have CVODES support
before trying to use it.
* R/diversitree-branches-C.R: Expose toC.int(). New do
asr.marginal.C(), for doing faster ASR.
* configure.ac: Changes to detect CVODES presence.
* configure.win: Disable CVODES.
* src/cvodes*: Check to see if CVODES enabled (WITH_CVODES)
* src/cvodes/cvodes_lapack.c: Minor fix to align with R's Lapack
* src/sundials_config.h: Disable unused sections
* src/.../sundials_lapack.h: Remove F77 cludging and use R's Lapack
2011-05-11 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: Bump version number to 0.7-1, and require deSolve >=
1.7.
* NAMESPACE: New make.asr.* functions around the different asr
functions (more changes to ASR code coming soon)
* README;cvodes-notes.txt: Information about CVODES
* configure.ac;configure.win;cleanup: Copy/delete CVODES files
when building and cleaning up. Strict GCC checks now enabled
whenever configure detects GCC is being used.
* R/asr-bisse.R;R/asr-mkn.R;R/asr-musse.R: More flexible root
treatment now possible.
* R/asr.R: New make.asr.* functions around the different asr
functions (more changes to ASR code coming soon). Switch internal
data from list to matrix.
* R/check.R: New check.control.ode() function for testing the ODE
tuning parameters. check.scalar() for checking things are length
1.
* R/cvodes.R;R/diversitree-branches-C.R: Support for the new
CVODES integrator.
* R/diversitree-branches.R: ROOT.EQUI was only using the
stationary frequency of state 0 (thanks to Gregory Imholte for
reporting). New function make.ode.branches(), which is the
preferred way of making branches functions. Allows switching
between the deSolve and CVODES integrators.
* R/model-bd-*.R;R/model-bisse*;R/model-geosse.R;R/model-musse*:
New CVODES integrator and branches interface added.
* R/t.R: make.ode.branches.t() is the new preferred way of making
time-dependent branches functions.
* R/util.R: Massive cleanup of the make.ode function. Will not
fail when using unknown deSolve, but will fall back on safe
version with a warning. Support for deSolve < 1.7 removed, and
support for deSolve 1.10 confirmed.
* inst/include: CVODES header files that are needed for making
CVODES based models.
* man/*: Documentation updates.
* src/Makevars.in;src/Makevars.win: New include flags needed for
CVODES
* src/bd-eqs.c;src/bisse-eqs.c;src/geosse-eqs.c;src/musse-eqs.c:
Support for CVODES models added.
* src/cvodes: Almost entirely unmodified CVODES package.
* src/cvodes_*: Wrapper around CVODES.
2011-04-20 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* NAMESPACE: new ROOT.MAX constant for maximising the root
state probability
* R/check.R: Simple support for multistate/polymorphic tip
states. Slightly improved "almost-integer" checking.
* R/mle.R: Additional arguments not being passed through to
hessian calculations.
* R/model-bisse-split.R: Work around corner case.
* R/model-bm.R: Check on parameter length. Don't require an
ultrametric tree. Measurement error handling was slightly off.
* R/model-musse.R: Simple support for multistate/polymorphic tip
states.
* man/constants.Rd: Added ROOT.MAX
* man/make.quasse.Rd: Update correct likelihood numbers. Disable
fftR run, as it is far too slow.
2011-03-17 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* data/geosse.R: Remove save=TRUE argument from require()
(defunct in R 2.13).
2011-03-14 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: Version bump to 0.6-4
2011-03-11 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* NAMESPACE: Added start of mkn-with-derivatives.
* R/check.R: Check for negative branch lengths in trees.
* R/diversitree-branches.R: Better treatment of root when one
lambda value is zero (*Will change calculations*)
* R/model-{bd-ode,bd-t,bisse-split,bisse-t,bisse-td,bisse,
geosse,musse-split,musse,musse-t,musse-td,musse}.R (and associated
documentation): Replaced safe=FALSE argument with control list
that also allows controlling precision of integration and quality
of results.
* R/mcmc-hmc.R: Hamiltonian (Hybrid) Monte Carlo sampler. Not yet
wired up to work with mcmc().
* R/model-linear-deriv.R, man/make.mkn.deriv.Rd,
src/linear-deriv.{c,h}: Preliminary code for mkn-with-derivatives
* src/util-complex.{c,h}, src/util-linalg.c,
src/util-matrix.{c,h}: Utilities for mkn-with-derivatives.
2011-02-18 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/mcmc.R: Removed check.par() from mcmc(). Changed order of
arguments for mcmc.lowerzero() to avoid an odd argument matching
bug.
* R/mle-mixed.R: Extra effort for QuaSSE models.
* R/model-quasse-split.R: Standardise attribute names
* R/util.R: Added count.eval(), added interval=0 support to
big.brother()
* man/asr-bisse.Rd, man/asr-mkn.Rd: Fixed examples
2011-01-26 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: Bumped to 0.6-3
* R/asr-musse.R: Added marginal ASR for MuSSE models
* R/model-geosse.R: Improved starting point function from Emma.
* R/model-musse.R, R/model-mkn.R: Support for models with >9
states (preventing duplicated argument names).
* R/util.R: deSolve 1.9 OK
* configure.win, src/Makevars.win, src/config.h.win: Hopefully
fixed windows build.
2010-10-25 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/check.R: No longer check node labels by default (duplicates
are not a problem for non-split methods).
* R/model-quasse-mol.R, R/model-quasse-common.R, R/model-quasse.R:
Methods-of-lines integration now works, albeit slowly.
* R/util.R: deSolve 1.8.1 OK
* cleanup: added
* configure.win, src/Makevars.win: Hopefully build on windows
(untested).
2010-10-21 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* many: Added GeoSSE to the package.
2010-10-20 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* many: Added QuaSSE to the package, including the configure build
system.
2010-10-14 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* NAMESPACE: new exports from below
* R/model-bd-ode.R: New ODE based version of the BD model; this is
really here for completeness and testing against the ODE based BD
extensions.
* R/model-bd-split.R: Removed find.mle method; inherits bd method
now.
* R/model-bd-t.R, R/model-bisse-t.R, R/model-musse-t.R: New
time-dependent models, where parameters are arbitrary functions
of time.
* R/model-bisse.R: Avoid warning when making bisse likelihood
function when all tips represent unresolved clades (thanks: Hanno
Schaefer for finding bug). Internal C function names have
standardised now.
* R/t.R: Support functions for time-dependent models.
* man/make.bd.R: Documentation for make.bd.ode()
* man/make.bd.split.R: Improve example
* man/make.bd.t.Rd, man/make.bisse.td.Rd, man/make/musse.td.Rd,
man/time.Rd: Add new time-varying functions to the help.
* man/mcmc.Rd: Small improvements in the help.
* src/bd-eqs.c: New file for ODE based BD model
* src/bisse-eqs.c: Standardised function names, and abstracted
derivative calculation from plain BiSSE, added time-dependent
derivative calculation.
* src/mkn.c: Moved matrix multiplication code into util.c
* src/musse.c: Abstracted plain MuSSE calculation, removed matrix
multiplication, added time-dependent derivative calculation.
* src/util.{ch}: Utility matrix multiplication helpers.
2010-09-23 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* NAMESPACE: new exports from below
* R/check.R: Improved logic of states checking for clade trees.
* R/clade.tree.R: make.unresolved() -> make.unresolved.bisse(),
plus similar function for bd models. Fixed an old bug, for where
clade trees do not include clades for *every* tip.
* R/mcmc.R: Added mcmc.lowerzero(), which is just passes through
to mcmc.default() with lower=0. This is used as the mcmc method
for all the likelihood models.
* R/model-bd-split.R: bd.split models now inherit from "bd".
* R/model-bd.R: Allow clade trees when making bd models.
2010-09-22 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: Bumped version number to 0.5-3, which will be
released soon. Also updated the description, and added "Suggests"
dependencies on multicore and tgp.
* NAMESPACE: New exports for the musse.split, musse.td models, and
generic mcmc.
* R/check.R: New check.par.length() for doing simple recycling.
Simplified check.sampling.f() to use this. Added
check.sampling.f.split(), check.bounds(), check.par.multipart().
* R/diversitree-branches.R: More defensive node depth/height
calculations when building cache.
* R/mcmc.R, R/mcmc-norm.R, R/mcmc-slice.R: New generic mcmc
function. Default method allows different MCMC samplers. Slice
sampling removed (added to R/mcmc-slice.R), and demonstration
univariate Gaussian sampler added. In mcmc(), 'lower', 'upper',
and 'w' can be passed in as scalars now.
* R/mle-tgp.R: New find.mle interface to the tgp statistical
optimiser (currently experimental and unadvertised).
* R/mle.R: Added support for tgp (see above). Simplified things
with new R/check.R support.
* R/model-bisse-split.R: BiSSE/split functions now inherit from
'bisse'. argnames.bisse.split() simplified.
find.mle.bisse.split() no longer required.
* R/model-bisse-td.R: Added 'safe' argument to make.bisse.td().
Changed argument order. Use check.par.multpart() to tidy
likelihood function. Simplify argnames.bisse.td(). Remved
find.mle.bisse.td().
* R/model-bisse.R: Switched 'safe' and 'strict' arguments for
consistency (should affect few users, as these should not really
be used positionally).
* R/model-musse-split.R, R/model-musse-td.R: Added new models.
* R/model-musse.R: Added 'safe' argument. Other minor changes.
* R/split.R: split.t can now be a scalar if '0' or 'Inf'.
* R/util.R: Added support for deSolve version 1.8. Added
make.prior.ExpBeta() (unadvertised, unexported), which gives an
alternative parametrisation of bisse models. Other support
functions added.
* man/make.bd.split.Rd, man/make.bisse.td.Rd,
man/make.musse.split.Rd, man/make.musse.td.Rd: new documentation files
* man/mcmc.Rd: Substantial rewrite to reflect new MCMC approach.
* man/make.bisse.Rd, man/make.musse.Rd: Minor cleanups
2010-08-12 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: Bumped version number to 0.5-2
* R/model-bd-split.R: make.bd.split has new default for split.t,
copying MEDUSA's default behaviour.
* R/split.R: Fixed bug in negative branch check.
* src/bucexp.f, src/dmexpv.f, src/dsexpv.f, src/dsexpvi.f,
src/hyperg.f: Tidied code to remove compiler warnings.
2010-08-06 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/model-bd-split.R: Fixed local naming error (phy->tree).
* man/argnames.Rd: Example was broken with strict character
checking.
* man/make.bisse.Rd: Document strict character checking.
2010-07-27 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* NAMESPACE, R/model-bd-split.R: New bd.split model
* R/split.R: Improved handling of times around splits.
* R/split-recycle.R: Removed.
2010-07-20 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/model-bisse-split.R, R/split.R: Removed the recycling code.
* NAMESPACE: New exports for the BiSSE/td model.
* R/check.R: Strengthened state checking.
* R/diversitree-branches.R: Renamed xxsse.ll -> ll.xxsse
* R/model-bisse-split.R: Now includes parameter recycling.
* R/model-bisse-td.R: New model
* R/model-bisse.R, R/model-musse.R: Strict state checking, other
minor changes.
* R/split.R, R/split-recycle.R: Bulk of the parameter recycling
code.
* R/td.R: New time dependent code
2010-06-23 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/diversitree-branches.R: Many changes to all.branches to remove
handling of unresolved clades, and to move the internal data
structures to be lists (rather than matrices). New function
dt.tips.ordered for helping make initial conditions in the format
we now expect.
* R/mcmc.R: MCMC now returns samples if run to completion (oops)
* R/model-bisse-split.R: Now makes its own branches.aux(), changes
to unresolved clade handling, new list structure, and using the
generic all.branches.split in R/split.R
* R/model-bisse.R: Changed handling of unresolved clades, given
above changes. Changed initial condition format.
* R/model-mkn-legacy.R: Removed as I doubt that it is accurate at
all now.
* R/model-mkn.R: Removed unresolved clades, updated to list
structure.
* R/model-musse.R: Removed unresolved clades, updated to list
structure, new initial conditions.
* R/split.R: New generic all.branches.split() and
make.cache.split() functions.
* R/util.R: matrix.to.list() - convert matrix rows to list
elements.
* R/check.R: Moved check.unresolved into R/model-bisse.R
* R/asr.R, R/asr-bisse.R, R/asr-mkn.R: Changed handling of
unresolved clades, given above changes. R/asr.R is also updated
to the new list data structures.
* man/*.Rd: Sundry documentation changes.
* R/model-mkn-legacy.R: check in before removal.
2010-06-14 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/constrain.R: Better constraining of constrained functions.
* R/history.R: Fix plot.history to better return an ape-compatible
state.
* R/mcmc.R: MCMC now allows interrupt part-way through a chain, and
returns all completed points so far.
* R/make.bisse.split.R: Tweaks to fix argument handling.
* R/model-bisse.R: subplex is now the default ML search
algorithm.
* R/make-bm.R: Clean up pre-diversitree code.
* R/model-musse.R: subplex is now the default ML search
algorithm. Better checking to make sure that expected states are
present.
* R/profiles-plot.R: Work around for extremely thin CIs
* R/simulation.R: musse trees available to 'trees()'.
* R/split.R: Catch an edge case of root node type.
* R/util.R: mrca.tipset() now accepts character vector of tip
names.
* man/constrain.Rd: Updated to reflect constraining constrained
functions being allowed.
* man/make.bisse.Rd: Removed prior argument from returned function
description.
* man/make.bisse.split.Rd: New help file.
* man/make.bm.R: New help file
* man/make.musse.Rd: Added starting.point.musse(), clarified
example.
* man/mcmc.Rd: MCMC interrupt documentation, new prior
requirements.
* man/simulate.Rd: Added Musse abilities.
2010-05-31 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* NAMESPACE: Added functions for the changes included in this
changeset.
* DESCRIPTION: bumped version number to 0.5-1, as this version
will have quite a few new features.
* R/clade-tree.R: New function clades.from.classification(), that
builds a clade tree by using a higher-level classification of
tips. Renamed polytomies.to.clades() -> clades.from.polytomies()
for consistency.
* R/clade-tree-plot.R: Removed - now uses alternative plotting in
R/plot-alt.R. Methods for control have been added to
R/clade-tree.R.
* R/history.R: Minor changes to cope with changes to the
alternative plotting interface.
* R/mcmc.R: Changes to move the prior control within MCMC.
* R/mle.R: Added box constraints for subplex (not done "properly",
but through disallowing any value outside of the constraints).
* R/model-bd.R: Moved to new checking functions in R/check.R,
using the "prior" argument to bd likelihood functions is now an
error.
* R/model-bisse.R: nt.extra was not being passed through
correctly. Moved to new checking functions, and added error for
use of "prior" argument to likelihood function.
* R/model-bm.R: Added to the package
* R/model-mkn-legacy.R: Added error for use of "prior" argument to
likelihood function.
* R/model-mkn.R: Moved to new checking functions, and added error
for use of "prior" argument to likelihood function.
* R/model-musse.R: Added to the package.
* R/plot-alt.R, R/plot-alt-util.R, R/plot-alt-extra.R: Completely
reworked. Now works for type="fan".
* R/simulate-musse.R: Added to the package
* R/split.R, R/model-bisse-split.R: Functions for partitioned,
MEDUSA-style, calculations, including the BiSSE method.
* R/util.R: New functions boxconstrain(), descendants(),
mrca.tipset(), and branching.heights() (none are exported).
* src/musse-eqs.c: Added to the package
* man/make.bd.Rd: Fixed typo in example
* man/make.clade.tree.Rd: Added documentation for
clades.from.classification(), though this is preliminary, and no
examples are given.
* man/make.musse.Rd: Added
* man/tree.musse.Rd: Added
2010-03-25 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* DESCRIPTION: bumped version number (did I miss checking in
0.4-5?)
* R/asr-mkn.R: Pass additional arguments through to underlying
likelihood calculations.
* R/model-bd.R: Some warnings for the Yule function with sampling
and unresolved clades. Fixed a couple of bugs (e.g., use of phy
rather than tree leading to unbound variables). Check parameter
number and give a nice error if the wrong number are given.
Corrected formula for bd likelihood under sampking where survival
is not conditioned on.
* R/profiles-plot.R: Overhaul that should perform much better on
distributions whose density does not tend to zero as x->infty.
Also now the shading lines up properly with the confidence
intervals.
* man/make.bd.Rd, man/make.bisse.Rd: Documentation improvements.
2010-03-02 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/model-bd.R: Fix for lambda=mu (not pretty, but should work in
the short term).
* R/mle.R: Reverted previous change (gives error when starting
point invalid) as the handling of '...' needs fixing.
* R/model-bd.R: Added support for sampled trees and trees with
unresolved clades.
* R/model-bisse.R: Minor logical tweaks in make.cache checking
code.
* R/simulate-bd.R: Don't create final species when making a tree
with fixed number of species (simulate to n+1 and trim the final
species).
* man/make.bisse.Rd: More examples, showing that BiSSE reduces to
Mk2 and the birth-death model under certain conditions. This is
also shown for the case of sampled trees and unresolved clades,
and acts as a good test case that everything is working
correctly.
* src/bucexp.f: Likelihoods were incorrectly calculated for clades
with no known states.
2010-02-23 Rich FitzJohn <fitzjohn@zoology.ubc.ca>
* R/asr*.R: Finished fix of the asr code.
* R/constrain.R: More informative error message when parameters of
wrong length.
* R/mle.R: find.mle gives error when starting point invalid.
* R/model-bisse.R, R/model-mkn.R: Give informative error message when
given invalid tree object (e.g. NULL) and likelihood calculations
give informative message when given wrong length parameters.
* R/zzz.R: no longer needed - removed.
* DESCRIPTION: Depend on at least deSolve 1.5, so that correct